chr8-8738102-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000522213.5(ENSG00000254367):​n.625-14368G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,030 control chromosomes in the GnomAD database, including 2,562 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.17 ( 2562 hom., cov: 32)

Consequence


ENST00000522213.5 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.240
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000522213.5 linkuse as main transcriptn.625-14368G>A intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.165
AC:
25096
AN:
151914
Hom.:
2557
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.297
Gnomad AMI
AF:
0.0758
Gnomad AMR
AF:
0.120
Gnomad ASJ
AF:
0.130
Gnomad EAS
AF:
0.110
Gnomad SAS
AF:
0.102
Gnomad FIN
AF:
0.140
Gnomad MID
AF:
0.228
Gnomad NFE
AF:
0.111
Gnomad OTH
AF:
0.160
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.165
AC:
25113
AN:
152030
Hom.:
2562
Cov.:
32
AF XY:
0.163
AC XY:
12133
AN XY:
74308
show subpopulations
Gnomad4 AFR
AF:
0.296
Gnomad4 AMR
AF:
0.120
Gnomad4 ASJ
AF:
0.130
Gnomad4 EAS
AF:
0.110
Gnomad4 SAS
AF:
0.101
Gnomad4 FIN
AF:
0.140
Gnomad4 NFE
AF:
0.111
Gnomad4 OTH
AF:
0.160
Alfa
AF:
0.121
Hom.:
654
Bravo
AF:
0.169
Asia WGS
AF:
0.128
AC:
445
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.43
DANN
Benign
0.19

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs554241; hg19: chr8-8595612; API